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MB Sample ID: SA299538
| Local Sample ID: | KPC_NT_2 |
| Subject ID: | SU002898 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Not applicable |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002898 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Gender: | Not applicable |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| KPC_NT_2 | SA299538 | FL036375 | sgNT | Genotype |
| KPC_NT_2 | SA299538 | FL036375 | KPC_FC1245 | Cell Line |
Collection:
| Collection ID: | CO002891 |
| Collection Summary: | On day 2, cells were harvested on ice by washing them once in ice-cold saline solution (9 g/l NaCl). Cells were covered with 250 μl of pre-cooled 80% methanol for 2 minutes scraped, transferred to fresh vials, and precipitated overnight at -80°C. Then they were centrifuged at 20.009 g for 15min, 4 degrees C and supernatant transferred to an M/S vial. |
| Sample Type: | Cultured cells |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002907 |
| Treatment Summary: | Cancer cells were cultured in DMEM medium supplemented with 10% FBS and 1% Pen/Strep in 6-well plates. On day 1, the cells and empty wells (for background noise control), were washed with PBS, and replenished with DMEM containing 10% FBS, 1% Pen/Strep, 5.5 mM glucose, 2 mM glutamine, 1% Pen/Strep, 0.1 mM cytidine (Sigma-Aldrich), or alternately, 0.1 mM labelled cytidine (13C9, 98% 15N3, 96-98%, Eurisotop) for 48h. |
Sample Preparation:
| Sampleprep ID: | SP002904 |
| Sampleprep Summary: | The samples were centrifuged at 20.000 x g for 15 min at 4°C, supernatant was transferred to appropriate M/S vial for analysis. The cell pellet was dissolved in 100 μl of 200 mM NaOH (for 20 minutes at 95°C), and the protein concentration was determined by using bicinchoninic acid (BCA) reagent method. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004541 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters Acquity UPLC HSS T3 (150 x 2.1mm, 1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | NEGATIVE |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH003411 |
| Chromatography Summary: | C18 IP REVERSE PHASE |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity UPLC HSS T3 (150 x 2.1mm, 1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | The gradient started with 5% solvent B and 95% solvent A and remained at 5% B until 2min post injection. A linear gradient to 37% B was carried out until 7min and increased to 41% until 14min. Between 14 and 26 minutes the gradient increased to 95% of B and remained at 95% B for 4 minutes. At 30 min the gradient returned to 5% B. The chromatography was stopped at 40 min. |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 100% water; 10mM tributylamine; 15mM acetic acid |
| Solvent B: | 100% methanol |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004288 |
| Analysis ID: | AN004541 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | EI-Maven polly, ThermoFisher Xcalibur, Metabolites were annotated using the inhouse standard metabolite library- elution time and m/z values. |
| Ion Mode: | NEGATIVE |
